4FNN

Crystal structure of the complex of CPGRP-S with stearic acid at 2.2 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis of the binding of fatty acids to peptidoglycan recognition protein, PGRP-S through second binding site.

Sharma, P.Yamini, S.Dube, D.Singh, A.Mal, G.Pandey, N.Sinha, M.Singh, A.K.Dey, S.Kaur, P.Mitra, D.K.Sharma, S.Singh, T.P.

(2013) Arch Biochem Biophys 529: 1-10

  • DOI: https://doi.org/10.1016/j.abb.2012.11.001
  • Primary Citation of Related Structures:  
    3T2V, 3UIL, 3UMQ, 3USX, 4FNN

  • PubMed Abstract: 

    Short peptidoglycan recognition protein (PGRP-S) is a member of the mammalian innate immune system. PGRP-S from Camelus dromedarius (CPGRP-S) has been shown to bind to lipopolysaccharide (LPS), lipoteichoic acid (LTA) and peptidoglycan (PGN). Its structure consists of four molecules A, B, C and D with ligand binding clefts situated at A-B and C-D contacts. It has been shown that LPS, LTA and PGN bind to CPGRP-S at C-D contact. The cleft at the A-B contact indicated features that suggested a possible binding of fatty acids including mycolic acid of Mycobacterium tuberculosis. Therefore, binding studies of CPGRP-S were carried out with fatty acids, butyric acid, lauric acid, myristic acid, stearic acid and mycolic acid which showed affinities in the range of 10(-5) to 10(-8) M. Structure determinations of the complexes of CPGRP-S with above fatty acids showed that they bound to CPGRP-S in the cleft at the A-B contact. The flow cytometric studies showed that mycolic acid induced the production of pro-inflammatory cytokines, TNF-α and IFN-γ by CD3+ T cells. The concentrations of cytokines increased considerably with increasing concentrations of mycolic acid. However, their levels decreased substantially on adding CPGRP-S.


  • Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan recognition protein 1
A, B, C, D
171Camelus dromedariusMutation(s): 0 
UniProt
Find proteins for Q9GK12 (Camelus dromedarius)
Explore Q9GK12 
Go to UniProtKB:  Q9GK12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GK12
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
STE
Query on STE

Download Ideal Coordinates CCD File 
E [auth B]STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
STE PDBBind:  4FNN Kd: 27.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.309α = 90
b = 101.436β = 90
c = 162.984γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description